Zoogeography of the Southeast Asian Rotifera

The distribution and taxonomic composition of Rotifera in Southeast Asia is reviewed. For some countries, records are poor: Brunei, Cambodia and Laos are almost terra incognitafor rotifers (<10 taxa recorded), while the Thai rotifer fauna is the best documented (ca. 310 taxa on record). However, analysis of the available data is impeded by fuzzy taxonomy and the questionable reliability of many records. Most studies focus on the pelagic or littoral of freshwater habitats. Other habitats are largely ignored. Similarly, few studies deal comprehensively with illoricate Monogononta, sessile Flosculariacea and Collothecacea and, especially, Bdelloidea. The genera Lecane, Brachionus and Trichocerca are the best represented, with littoral taxa predominant. Fisheries-related studies dealing with highly productive pelagic environments tend to over report the contribution of Brachionus. Most taxa are thermophilic character, exemplified by the dominance of tropic-centred Lecaneand Brachionus. Some cold-water taxa have been recorded, but the relative climatological homogeneity of the region and low number of studies on high-altitude environments prevent the discrimination of clear latitudinal or altitudinal variation in the distribution of rotifers within Southeast Asia. The majority of Southeast Asian rotifers are widely distributed, including true cosmopolites and thermophilic taxa. There are several local or Oriental endemic Rotifera, mostly Lecane. The American Brachionus havanaensis and Keratella americana appear to have been introduced to the region. The taxonomy of some Rotifera described from the region is commented upon; Brachionus murphyiSudzuki is recognised as senior synonym of B. niwati Sanoamuang et al. (syn. nov.). Some cases of geographical and/or ecological vicariant species-pairs are suggested. The Southeast Asian rotifer fauna contains a sizeable fraction of taxa occurring in the tropical regions of the Old World, most of which also occur in tropical Australia or the Austro-Malayan region. A tropical Australasian faunal component is present, but consists of few taxa only. Hence, affinities between the rotifer fauna of the Ethiopian, Oriental and tropical Australian and Austro-Malayan regions are supported, rather than an affinity between the Indo-Asian or Indo-Malaysian and tropical Australian fauna.     

High throughput sequencing enables discovery of microsatellites from the puff-throated bulbul (Alophoixus pallidus) and assessment of genetic diversity in Khao Yai National Park,Thailand

Bulbuls (family Pycnonotidae) are a diverse family of songbirds that carry out a number of ecologically important functions associated with seed dispersal. Since, 2003, a puff-throated bulbul (Alophoixus pallidus) population in the Mo-Singto Long-term Biodiversity Research Plot in Khao Yai National Park, Thailand has served as a model system for examining how bulbul behavior, movement, and demographics affect Southeast Asian forests. In this study, we used 454 pyrosequencing to discover microsatellites from A. pallidus that will enable the long-term mark-recapture work conducted at Mo-Singto to be complemented by molecular ecology and population genetic studies. In addition, we conducted fragment analysis to examine the level of genetic diversity exhibited by the Mo-Singto population. In total, we identified 103 DNA fragments containing microsatellite repeats and 66 fragments with sufficient flanking sequences to allow for primer design. Upon screening 26 loci via PCR-based genotyping assays, we identified nine polymorphic loci and used eight of these to examine genetic diversity in the Mo-Singto population. The results of these analyses suggest that the Mo-Singto population is moderately diverse (mean number of effective alleles across eight loci = 3.36, standard deviation = 1.78), is more-or-less in Hardy–Weinberg equilibrium, and has not recently been subject to severe population reduction.     

Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography

Aim Using molecular data and dental features, we investigated the genetic and morphological diversity among species of palm civets in the genus Paradoxurus, with a focus on the common palm civet, Paradoxurus hermaphroditus (Carnivora, Viverridae), in order to address biogeographic scenarios and provide recommendations for a taxonomic revision. Location Asia: Pakistan to the Lesser Sunda Islands. Methods We investigated the genetic diversity within Paradoxurus using two mitochondrial (cytochrome b, control region) and one nuclear (intron 7 of the β‐fibrinogen) markers. We used samples from 85 individuals of P. hermaphroditus (including 20 museum specimens) and one representative of each of the other species in the genus Paradoxurus: Paradoxurus jerdoni and Paradoxurus zeylonensis. DNA sequences were analysed using phylogenetic and haplotype network methods, and divergence dates were estimated for the clades retrieved. Furthermore, we examined dental characters from a large series of specimens and compared the morphological variation with the molecular data. Results Our phylogenetic analyses revealed that P. hermaphroditus is paraphyletic. We identified three major lineages distributed: (1) in the Indian subcontinent, south China, Hainan and in areas above 200 m in Indochina; (2) in Peninsular Malaysia, Java, Sumatra and in areas below 200 m in Indochina; and (3) in Borneo, the Philippines and the Mentawai archipelago. Our morphological observations were congruent with these three molecular lineages. Divergence date estimates inferred a Pliocene origin for Paradoxurus (2.8–5.7 Ma), with the three main clades diversifying from the mid–Early Pliocene to the end of the Pliocene. We suggest that the flooding of the Isthmus of Kra during the Pliocene was a major event shaping the diversification of Paradoxurus palm civets. We also hypothesize that the elevational segregation of the two lineages on the mainland could have resulted from the vegetational changes that were induced by Late Pliocene glacial episodes. Main conclusions The Isthmus of Kra is a major boundary between two major lineages of P. hermaphroditus. There is a need for a taxonomic revision for P. hermaphroditus, and we suggest that this species should be split into at least three species.     

The Collothecidae (Rotifera,Collothecacea) of Thailand,with the description of a new species and an?illustrated key to the Southeast Asian fauna

Following previous reports indicating a remarkable high diversity of sessile rotifers in Southeast Asian freshwaters, we report on an extensive study of the diversity of Collothecidae rotifers from fifteen freshwater habitats in Thailand. A total of 13 species, including two additional infraspecific variants, of Collothecidae are recorded, one of which is described as a new species of Collotheca. We further add taxonomic remarks on some of the taxa on record and illustrate the uncinate trophi of several representatives by scanning electron microscopic images. Finally, we provide illustrated identification keys to the Collothecidae recorded to date from Southeast Asia.     

基因组时代的新视野: 东南亚哺乳动物类群在第四纪冰河时期多样性的起源与分化

东南亚地区东起菲律宾群岛, 西至印度次大陆, 北及中国中部, 南至巽他群岛, 涵盖了世界上25个最重要的生物多样性热点地区之中的6个, 具有极其重要的全球生物多样性保护的战略意义。该地区复杂的地质地貌和气候历史使其动植物的种类和数量都极为丰富。经典的生物地理分界线华莱士线和克拉地峡将该地区进一步划分出包括部分巽他群岛和马来半岛在内的南部巽他区和北部印度支那区两个生物多样性热点地区。主要基于形态学的生物地理学研究认为巽他区和印度支那区通过马来半岛陆地相连, 并且第四纪大部分时间海平面下降形成大陆桥, 直到一万年前该地区的众多岛屿仍与大陆连接, 促进了哺乳动物的种群迁徙与基因交流, 因此物种种群间的差别将很细微。然而近来分子遗传学研究表明, 由于其他生态因素制约, 哺乳动物的迁移能力可能比以往认为的低, 大陆桥的存在并不一定导致迁徙的发生, 许多种群的隔离早在200万年前便已形成, 并且没有因为后来冰川期海平面降低而恢复种群交流, 而距今7.3万年前发生的苏门答腊多巴超级火山爆发也可能进一步影响了物种间和物种内多样性的形成和分化。通过已有的东南亚哺乳动物种群遗传学研究结果, 我们认为物种间或种群间的差异主要表现为三个层次: 巽他区种群与印度支那区种群间约百万年尺度的分化, 巽他区不同岛屿种群间约数十万年尺度的分化, 以及发生于晚更新世的分化事件。已有的东南亚种群遗传学研究主要采用线粒体及核基因多位点数据进行分析, 而种群基因组学分析则使得获得详尽的种群历史动态成为可能, 并使我们可以进一步了解东南亚哺乳动物类群所经历的物种形成过程。     

东南亚兰科植物的物种多样性、生活习性及其传粉系统（附表）

兰科(Orchidaceae)植物广布于除两极和极端沙漠地区外的各种陆地生态系统,包括5个亚科800多属28 000多种。东南亚地区兰科植物种数约占世界的1/3,是兰科植物生物多样性热点区域之一。通过查阅文献及书籍等资料,该文系统整理了东南亚兰科植物物种种类及其扩散演化历史,并对其生活习性和传粉系统进行了归类。结果表明:(1)东南亚兰科植物8 855种,分属5亚科17族26亚族240属;(2)主要生活型为附生的有127属6 000种以上,地生97属2 000种以上,腐生13属约100种,藤本4属40余种;(3)根据整理出的东南亚79个属的兰科植物传粉系统发现,有44个属含有自动自交的物种,具报酬物的传粉系统有花粉(仅见于拟兰亚科)、芳香类物质(仅见于香荚兰亚科)和花蜜(5个亚科均有)等报酬物类型。欺骗性传粉系统广泛存在于各个亚科,包括食源性欺骗、性拟态、繁殖地拟态和信息素拟态等类型。东南亚兰科植物在物种、生活习性及传粉系统都展现出极高的多样性,对这些生物学特点的总结将为兰科植物的保育提供一定的理论基础和本底资料。     

Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA

Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome‐wide set of 753–4,501 variable loci and 3,919–18,472 single nucleotide polymorphisms. The formation of major within‐species lineages occurred within a similar span of time (0.5–1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east–west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high‐throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.     

The Indochinese–Sundaic zoogeographic transition: a description and analysis of terrestrial mammal species distributions

Aim We describe the distributions of mammal species between the Indochinese and Sundaic subregions and examine the traditional view that the two faunas show a transition near the Isthmus of Kra on the Thai–Malay peninsula. Location Species distributions are described along a 2000‐km transect from 20° N (northernmost Thailand) to 1° N (Singapore). Methods For the 325 species of native non‐marine mammals occurring along the transect we used published records to provide a database of their distributional records by degree of latitude. Results Along the transect we found 128 Indochinese species with southern range limits, 121 Sundaic species with northern range limits, four un‐assignable endemics and 72 widespread species. In total, 152 southern and 147 northern range limits were identified, and their distribution provides no evidence for a narrow faunal transition near the Isthmus of Kra (10°30′ N) or elsewhere. Range limits of both bats and non‐volant mammals cluster in northernmost peninsular Malaysia (5° N) and 800 km further north, where the peninsula joins the continent proper (14° N). The clusters of northern and southern range limits are not concordant but overlap by 100–200 km. Similarly, the range limits of bats and non‐volant mammals cluster at slightly different latitudes. There are 30% fewer species and range limits in the central and northern peninsula (between 6 and 13° N), and 35 more widely distributed species have range gaps in this region. In addition, we found 70 fewer species at the southern tip of the peninsula (1° N) than at 3–4° N. Main conclusions The deficiencies of both species and species range limits in the central and northern peninsula are attributed to an area effect caused by repeated sea‐level changes. Using a new global glacioeustatic curve developed by Miller and associates we show that there were > 58 rapid sea‐level rises of > 40 m in the last 5 Myr that would have resulted in significant faunal compression and local population extirpation in the narrow central and northern parts of the peninsula. This new global sea‐level curve appears to account for the observed patterns of the latitudinal diversity of mammal species, the concentration of species range limits north and south of this area, the nature and position of the transition between biogeographical subregions, and possibly the divergence of the faunas themselves during the Neogene. The decline of species diversity at the southern end of the transect is attributed to a peninsula effect similar to that described elsewhere.     

Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages

Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40–25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.     

Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600–1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.     

Multiple origins of parthenogenesis,and a revised species phylogeny for the Southeast Asian butterfly lizards,Leiolepis

Hybridization often occurs in areas of secondary contact between closely related species. In some cases these hybridization events can create hybrid offspring that are reproductively viable as new parthenogenetic species. The genus Leiolepis contains nine species that collectively range throughout continental Southeast Asia. Of these, four are unisexual (some diploid and some triploid). We analyzed a multi‐locus dataset within a multi‐lineage coalescent framework to infer the origins of these parthenogenetic hybrid species. Our results provide evidence that repeated hybridization events between L. reevesii and L. guttata have led to the formation of all four distinct parthenogenetic species. Our data further suggest there have been low levels of mitochondrial introgression between L. belliana and L. reevesii at their contact zone in southern Cambodia. This work addresses contentious species boundaries and provides the first taxon‐complete hypothesis of relationships for the butterfly lizards. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1080–1093.     

Genetic diversity and inferred ancestry of Asian lotus (Nelumbo nucifera) germplasms in Thailand and Vietnam

Tropical lotus (Nelumbo) is an important and unique ecological type of lotus germplasm. Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization. Using 42 EST-SSR (expressed sequence tag-simple sequence repeats) and 30 SRAP (sequence-related amplified polymorphism) markers, we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam. In total, 164 and 41 polymorphic bands were detected in 69 accessions by 36 EST-SSR and seven SRAP makers, respectively. Higher genetic diversity was revealed in Thai lotus than in Vietnamese lotus. A Neighbor-Joining tree of five main clusters was constructed using combined EST-SSR and SRAP markers. Cluster I included 17 accessions of Thai lotus; cluster II contained three Thai accessions and 11 accessions from southern Vietnam; and cluster III was constituted by 13 accessions of seed lotus. Consistent with the results from the Neighbor-Joining tree, the genetic structure analysis showed that the genetic background of most Thai and Vietnamese lotus was pure, as artificial breeding has been rare in both countries. Furthermore, these analyses indicate that Thai and Vietnamese lotus germplasms belong to two different gene pools or populations. Most lotus accessions are genetically related to geographical distribution patterns in Thailand or Vietnam. Our findings showed that the origin or genetic relationships of some unidentified lotus sources can be evaluated by comparing morphological characteristics and the data of molecular markers. In addition, these findings provide reliable information for the targeted conservation of tropical lotus and parent selection in breeding novel cultivars of lotus.     

Phylogenetic systematics of the viviparous halfbeak genera Dermogenys and Nomorhamphus (Teleostei:Hemiramphidae:Zenarchopterinae)

Among the 13 genera and over 100 species of halfbeaks, three genera - Dermogenys, Nomorhamphus and Hemirhamphodon – are internally fertilized and viviparous. These genera belong to a more inclusive clade, the Zenarchopterinae, that also includes Zenarchopterus , inferred to be internally fertilized and to lay fertilized eggs, and the monotypic Tondanichthys , also inferred to be internally fertilized. Whereas the Hemiramphidae are distributed worldwide, internally fertilized halfbeaks are restricted to Southeast Asia. Recent data from histological surveys of the gonads of both males and females as well as embryonic modifications associated with viviparity have been combined here with osteological characters in a phylogenetic analysis. Results indicate overwhelming support for a sister-group relationship between Hemirhamphodon and {Dermogenys + Nomorhamphus). Monophyly of the Dermogenys + Nomorhamphus clade is also well supported. These results confirm earlier suggestions that Dermogenys , as previously defined, is paraphyletic. Within the Dermogenys + Nomorhamphus clade, two monophyletic clades are supported:one comprises ten species including four new species (Dermogenys bruneiensis, Dermogenys robertsi, Dermogenys palawanensis and Dermogenys collettei) and the other comprises 13 species including three undescribed species (Nomorhamphus rossi, Nomorhamphus pinnimaculata and Nomorhamphus manifesta). Diagnoses for the species of Dermogenys and Nomorhamphus , as well as a natural classification for the included species, are presented.     

Historical biogeography of the Southeast Asian and Malesian tribe Dissochaeteae (Melastomataceae)

The region of Tropical Southeast Asia and the Malay Archipelago is a very appealing area for research due to its outstanding biodiversity, being one of the most species-rich areas in the world with high levels of endemism, and due to its complex geological history. The high number of species in tribe Dissochaeteae (Melastomataceae) and their tendency to narrow endemism makethe tribe an ideal group for examining biogeographic patterns. We sampled 58 accessions spread over 42 accepted and two undescribed species of the Dissochaeteae. Two nuclear (ETS, ITS) and four chloroplast regions (ndhF, psbK-psbL, rbcL, rpl16) were used for divergence time estimation and ancestral area reconstruction. Results from the molecular dating analysis suggest that the diversity of Dissochaeteae in the Southeast Asian region resulted from a South American ancestor in the late Eocene. The ancestor of the Dissochaeteae might have migrated from South America to Southeast Asia via North America and then entered Eurasia over the North Atlantic land bridge during the Eocene. The origin and early diversification of the Dissochaeteae in Southeast Asia dates back to the middle Oligocene, and most of the genera originated during the Miocene. Indochina and Borneo are most likely the area of origin for the most recent common ancestor of the Dissochaeteae and for many of the early diverging clades of some genera within Southeast Asia.